I want to apologize for wasting this forum space and admit to being a fool. It turns out the problem was never happening on my acekard to begin with - and it WAS happening whenever I saved on the supercard regardless of the size of the song.
See, I had the acekard for awhile before I ever got my supercard.
What happened was I made some stuff on the acekard, saved it, then after I got my supercard I opened the songs on there, added to them, then tried to save again and got the freeze. I assumed this was happening because I had tried to add to the song. I never experimented fully to see if this was really the problem - I just assumed that meant nitrotracker was mostly useless and stopped using it.
Turns out its a problem with the dldi patcher for the supercard lite. I had to use the supercard rumble miniSD patch instead, and now nitrotracker saves just fine on the supercard too. I can't express how glad I am that I found this out. I only wish I'd figured it out before i spent $15 on the mostly inferior korg ds-10. Its a nice little program, and it does have some complex synth controls that nitrotracker doesn't have but. . . only 16 tracks? seriously? And you can't even mute tracks in pattern instances in the song. . . by that I mean if you want to have an instrument start playing in your song, then after a few measures have another instrument come in while the first instrument is still playing the same thing, then have a bass drum beat come in after that, then add the snare/hat/whatever over the top of that. . . that's 4 of your 16 patterns right there. And you only get two pitch instruments! That is unless you tweak some stuff and sacrifice some of your drum tracks to turn them into instruments.
What I'm saying is Korg DS-10, while still very cool and a neat little game - just isn't going to cut it as a real on-the-go music composition tool. Nitrotracker DOES cut it, and now that I can actually save what I do in here I don't need to bother with that silly Korg DS-10 game cartridge anymore.
Sorry again for posting before really looking into what was going on.